Inferring the evolutionary history of a group of species can be challenging given the many factors involved. In recent years, the increased availability of sequences of multiple genes per species has spurred the development of new methodologies to analyse multilocus data sets. Two approaches that analyse such data are concatenated supermatrix and coalescent‐based species‐tree analyses. In this study, we used both of these methods to infer the phylogenetic relationships of Iberian species of the genus Squalius from one mitochondrial and six nuclear genes. We found mitonuclear discordance in the phylogenetic relationships of the group. According to the mitochondrial gene analysis, all species were recovered as monophyletic except S. pyrenaicus; besides, in the concatenated supermatrix analysis of the nuclear markers, this species resolved as polyphyletic with three divergent evolutionary lineages. The coalescent‐based nuclear species‐tree analysis rendered a well‐resolved phylogeny compared with the supermatrix analysis, which was unable to discern between S. carolitertii, S. castellanus and one of the evolutionary lineages of S. pyrenaicus. This result is likely due to the better integration of population uncertainty in the coalescent approach. Furthermore, Bayesian multilocus species delimitation analyses based on a BPP approach strongly supported the distinct nuclear lineages as different species. Nevertheless, the supermatrix analysis was able to obtain well‐supported relationships in the divergent lineages with low numbers of individuals. Our study highlights the usefulness of different analytical methodologies to obtain a more complete picture of the evolutionary history of taxa, especially when discordant patterns among genes are found.

中文翻译：

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伊比利亚特有的 Squalius (Actinopterygii, Leuciscidae) 的多位点系统发育和系统学

鉴于涉及的许多因素，推断一组物种的进化历史可能具有挑战性。近年来，每个物种的多个基因序列的可用性增加，刺激了分析多位点数据集的新方法的发展。分析此类数据的两种方法是连接超矩阵和基于聚结的物种树分析。在这项研究中，我们使用这两种方法从一个线粒体基因和六个核基因推断 Squalius 属伊比利亚物种的系统发育关系。我们在该组的系统发育关系中发现了线粒体核不一致性。根据线粒体基因分析，除S. pyrenaicus外，所有物种均恢复为单系；此外，在核标记的级联超矩阵分析中，该物种被解析为具有三个不同进化谱系的多系。与无法区分 S. carolitertii、S. castellanus 和 S. pyrenaicus 的进化谱系之一的超矩阵分析相比，基于聚结的核种树分析提供了一个很好解析的系统发育。这一结果可能是由于在合并方法中更好地整合了人口不确定性。此外，基于 BPP 方法的贝叶斯多位点物种定界分析强烈支持作为不同物种的不同核谱系。尽管如此，超矩阵分析能够在个体数量较少的不同谱系中获得良好支持的关系。